Research workbench
Structural basis for the target DNA recognition and binding by the myb domain of phosphate starvation response regulator 1
Analyse Structural basis for the target DNA recognition and binding by the myb domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6J4R
- Type
- protein + DNA
- Length
- 271 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein phosphate starvation response 1; DNA (5'-D(*CP*CP*AP*TP*AP*TP*AP*TP*GP*AP*C)-3')…
- UniProt
- Q94CL7
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 8 distinct chains · 62% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein phosphate starvation response 1 | protein | 58 | 66% helix, 0% strand | Q94CL7 |
| B | Protein phosphate starvation response 1 | protein | 57 | 60% helix, 0% strand | Q94CL7 |
| C | Protein phosphate starvation response 1 | protein | 55 | 62% helix, 0% strand | Q94CL7 |
| D | Protein phosphate starvation response 1 | protein | 57 | 60% helix, 0% strand | Q94CL7 |
| F | DNA (5'-D(*CP*CP*AP*TP*AP*TP*AP*TP*GP*AP*C)-3') | dna | 11 | — | — |
| E | DNA (5'-D(*GP*TP*CP*AP*TP*AP*TP*AP*TP*GP*G)-3') | dna | 11 | — | — |
| X | DNA (5'-D(*GP*GP*TP*AP*TP*AP*TP*AP*CP*TP*G)-3') | dna | 11 | — | — |
| Y | DNA (5'-D(*CP*AP*GP*TP*AP*TP*AP*TP*AP*CP*C)-3') | dna | 11 | — | — |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 556 | 0.71 | 0.80 | 50 | empty |
| 2 | 258 | 0.64 | 0.82 | 30 | empty |
| 3 | 142 | 0.45 | 0.77 | 24 | empty |
| 4 | 142 | 0.44 | 0.77 | 22 | empty |
| 5 | 70 | 0.36 | 0.78 | 11 | empty |
Interfaces
14 interfaces between chains.
- X–Y · 518 Ų buried · 50 hydrogen bonds · nucleic-nucleic
- F–E · 512 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- A–F · 492 Ų buried · 14 hydrogen bonds · protein-nucleic
- C–Y · 470 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–E · 438 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
- 6J4R · Structural basis for the target DNA recognition and binding by the MYB domain of… · the same entry in another collection · chain Y against Y, TM-score 1.00
- Q94CL7 · AlphaFold monomer V2.0 prediction for protein phosphate starvation response 1 (Q94CL7) · a predicted model of the same protein · chain C against A, TM-score 0.96
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q94CL7
- Elsewhere: RCSB PDB 6J4R · PDBe 6J4R · UniProt Q94CL7
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